Integrative analysis workflow for the structural and functional classification of C-type lectins

Abstract

Background: It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles.

Results: Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner.

Conclusions: The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments.

Figure 1

Analysis workflow. A schematic illustration of the integrated workflow. The left side of the panel summarizes the steps for the sequence and structural characterization of novel C-type lectins at various levels. The right side shows equivalent analyses for glycans that is needed in order to construct a virtual library amenable for virtual screening.

Figure 2

Construction of in silico library. The glycans from the array are listed out (in the modified condensed IUPAC format) and submitted to our glycan modeling server for generating conformers that are amenable for docking studies.

Figure 3

Features of CLEC17A. Summary of the relevant features found along the sequence of CLEC17A.

Figure 4

Predicted structure of CLEC17A. (A) Homology modeling of CLEC17A and the score of its structure calculated by Profiles-3D. (B) Ramachandran plot of the psi-phi angles between all amino acid residues of the predicted. Most of the residues fall within allowed regions (95.7%), a small percentage of residues are within the marginal regions (3.4%), and only 3 residues are located in the disallowed region (0.9%).

Figure 5

Virtual screening of CLEC17A against the in silico glycan library. (A) Binding sites on CLEC17A that were screened against the glycan library. (B) Structure of a glycan terminating with mannose bound to site 2 on CLEC17A. (C) Proportion of the glycans in the library terminating with the respective monosaccharides, and having plausible poses on binding sites 1 and 2.